BetaStability Quick Start Guide

In betaStability: Quantify the Compositional Stability of Each Community Based on a Single Sampling Event

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BetaStability Quick Start Guide

This vignette demonstrates the capabilities of the BetaStability package using the varespec and varechem datasets from the vegan package.

Installation

First, install the package from GitHub:

# Install from GitHub
# install.packages("devtools")
# devtools::install_github("gaoyu19920914/betaStability")

# OR install from BioConductor (in the future when it's available)
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# BiocManager::install("betaStability")

Loading Required Packages

Load the BetaStability package and the vegan package for test data:

library(betaStability)
library(vegan)
library(ggplot2)

Loading Test Data

Load the varespec (community data) and varechem (environmental metadata) datasets from the vegan package:

data(varespec)
data(varechem)

# Inspect the data
head(varespec)
head(varechem)

# Dimensions of the datasets
cat("Dimensions of varespec:", dim(varespec), "\n")
cat("Dimensions of varechem:", dim(varechem), "\n")

Calculating Stability with Single Method

Calculate stability using a single prediction method (linearPred):

# Calculate stability with linearPred
result_linear <- betaStability(
    comtable = varespec,
    envmeta = varechem,
    method = "linearPred"
)

# Inspect the result
head(result_linear)
length(result_linear)

Calculating Stability with Multiple Methods

Calculate stability using multiple prediction methods:

# Calculate stability with multiple methods
results_multi <- betaStability(
    comtable = varespec,
    envmeta = varechem,
    method = c("linearPred", "mlPred", "glmPred")
)

# Inspect the result
head(results_multi)
dim(results_multi)

Calculating Stability with All Methods

Calculate stability using all available prediction methods:

# Calculate stability with all methods
results_all <- betaStability(
    comtable = varespec,
    envmeta = varechem,
    method = "all"
)

# Inspect the result
head(results_all)
dim(results_all)
colnames(results_all)

Visualizing Stability Results

Visualize the stability results using the plotStability function:

# Plot stability results for single method
p1 <- plotStability(result_linear)
p1

# Plot stability results for multiple methods
p2 <- plotStability(results_multi)
p2

# Plot stability results for all methods
p3 <- plotStability(results_all)
p3

Customizing Site Names

You can also customize the site names in the plot:

# Create custom site names
custom_sitenames <- paste("Site", seq_len(nrow(varespec)))

# Plot with custom site names
p4 <- plotStability(results_multi, sitenames = custom_sitenames)
p4

Conclusion

The BetaStability package provides a comprehensive framework for calculating and visualizing site stability using various prediction methods. Key features include:

1. Multiple prediction methods: Choose from linear, multiple linear model, generalized linear model, generalized additive model, generalized dissimilarity model, random forest, and xgboost models.
2. Flexible input options: Use precomputed distance matrices or let the package compute them automatically.
3. Easy visualization: The plotStability function creates informative plots of stability results.
4. Convenient "all" method: Run all prediction methods with a single parameter setting and receive a summary of results.

This package is designed to help researchers and ecologists assess site stability based on the beta stability of communities, providing valuable insights for ecosystem management.

print(sessionInfo())

betaStability documentation built on June 5, 2026, 5:08 p.m.